The nicotinic acetylcholine receptor (AChR) is the prototype of ligand-gated ion channels. Here, we calculate the dynamics of the muscle AChR using normal modes. The calculations reveal a twistlike gating motion responsible for channel opening. The ion channel diameter is shown to increase with this twist motion. Strikingly, the twist motion and the increase in channel diameter are not observed for the AChR in complex with two α-bungarotoxin (αBTX) molecules. The toxins seems to lock together neighboring receptor subunits, thereby inhibiting channel opening. Interestingly, one αBTX molecule suffices to prevent the twist motion. These results shed light on the gating mechanism of the AChR and present a complementary inhibition mechanism by snake-venom-derived α-neurotoxins.Predicting protein dynamics is essential for a better understanding of many biological processes. One of the standard techniques for studying protein dynamics and, in particular, low-frequency domain motions is normal-mode analysis. In contrast to molecular dynamics, normal-mode analysis provides a very detailed description of the dynamics around a local energy minimum. Even with its limitations, such as the neglect of the solvent effect, the use of harmonic approximation of the potential energy function, and the lack of information about energy barriers and crossing events, normal modes have provided much useful insight into protein dynamics. Over the past years, several techniques have been described to calculate large-scale motions using simplified normal-mode analysis (1-3). The Internet also contains a number of interactive programs to calculate normal modes, such as the elastic network model (4), ElNemo (5), and GROMACS (6).The nicotinic acetylcholine receptor (AChR) 1 is a ligand-gated ion channel that is opened by the neurotransmitter acetylcholine (ACh). Channel opening is associated with an ion flux, leading to neuromuscular transmission. The AChR consists of five subunits in the stoichiometry, α 2 δβγ, arranged in a clockwise order around the ion channel (7). The receptor has two ACh-binding sites, a higher affinity site at the interface of α and δ subunits, and a lower affinity site at the interface of α and γ subunits (8). Binding in these sites is cooperative, and channel opening occurs only when both sites are occupied (8). The ACh-binding sites are also the target of a variety of agonists, such as nicotine and epibatidine, and antagonist, such as † This research was supported by National Institutes of Health (NIH) Roadmap 2PN2-EY016525, NIH Grant GM41455, and NSF award CNS-0619926 for computer resources.*To whom correspondence should be addressed. Telephone: (650) 725-0754. Fax: (650) 723-8464. E-mail: michael.levitt@stanford.edu.
SUPPORTING INFORMATION AVAILABLEMovies of the normal-mode vibration of the AChR and it's complex with αBTX. This material is available free of charge via the Internet at http://pubs.acs.org. 1 Abbreviations: MD, molecular-dynamics; NMA, normal-mode analysis; NMR, nuclear magnetic resonance; α B...